Automated Model Building

This new, beta-version module has the same aims as ARP/wARP Classic: to automatically build protein structures, starting either from molecular replacement models or experimental electron density maps.

The only important difference is on the Sequence file. If you have hetero-multimers in the asymmetric unit of your crystals, you should add each sequence separately, by clicking the Add Input PIR file button. Then, you can then define any stoichiometry for complicated hetero-multimers. For each defined sequence the user can select from a pull-down menu the number of copies in the asymmetric unit. Based on that and the contents of the PIR file the contents of the AU in residues is calculated automatically.

The input files are identical to the ARP/wARP Classic module.

There is a dedicated option to select that the Methionines are Se-Met residues if the dataset comes from a SAD or MAD experiment on a selenium edge.

The Decision parameters are where the innovative choices for controlling ARP/wARP are given. The number of refinement and building cycles are not fixed, but they are defined on the fly based on program’s progression. The Decision parameters are defining these limits. If you leave the mouse over one of the input fields, a help text will appear explaining the use of each decision parameter.

The parameter maximum number of processes in parallel is important and is briefly explained below. When Flex-wARP decides that it has reached a more-or-less useful model, it will spawn a 'cleaning up and completion' process. However it will continue the iterative building in parallel. If the iterative building results in a better model, a new 'cleaning up and completion' process will be requested, possibly before the previous 'cleaning up and completion' process has finished. If you have only two processors (typical these days in dual core systems) the new process will be 'queued'; when the previous one is finished the new one will start.

We emphasise that the Flex-wARP module is new and ‘experimental’. We hope that in the future we will be able to offer more tricks and tips.

Running model building from command line

Usage: CAutoPyWARP.pyc [--param_file=<FILE>] | [--mode=<MTZ|PDB2MTZ|PDBDummyAll|PDBStart> --datafile=<FILE> --modelin=<FILE> --seqin=<FILE1:NCS1:FILE2:NCS2...> --fp=<FP label> --sigfp=<SIGFP label> --fstart=<F label for initial map> --phistart=<PHI label for initial map> --hla=<HLA label> --hlb=<HLB label> --hlc=<HLC label> --hld=<HLD label> --free=<Free_Set label> --workdir=<DIRECTORY> --title=<"title of the run">]

Options:

--version show program's version number and exit

-h, --help show this help message and exit

--param-file=FILENAME

A parameter file containing values for the parameters.

--title=STRING The title to use for the job, do not forget to quote

or escape the spaces...

--workdir=DIRECTORY The name of the directory in which the program should

be run.

The mode to run CPyWARP in.

--datafile=FILENAME The MTZ file to use through out the building.

--modelin=FILENAME For mode PDB or PDB2MTZ : the model to use to start

from.

--mr-modelin=FILENAME:IDENTITY:NUMBEROFCOPY:...

For modes MR_... : a list of model files with the

corresponding parameters to use for Moleculare

Replacement.

--seqin=FILENAME:NCS:...

A list of sequence file with the corresponding

multiplicity (ie. --seqin=seq1.pir:2:seq2.pir:4).

--final-model=FILENAME

Setting the name of the final model that should be

used to derive statistics.

--fp=LABEL The label of the observed amplitudes (natives).

Default FP.

--sigfp=LABEL The label of the estimate of the sigma of the native

amplitude. Default SIGFP.

--fstart=LABEL Label of the amplitude to use (together with phistart

and fomstart) for computing the first map (solvent

flattened map). Default FDM.

--phistart=LABEL Label of the phase to use (together with fstart and

fomstart) for computing the first map (solvent

flattened map). Default PHIDM.

--fomstart=LABEL Label of the FOM to use (together with fstart and

phistart) for computing the first map (solvent

flattened map). NO default.

--hla=LABEL Label of the H.L. A coef. to use during phased

refinement in refmac. NO default.

--hlb=LABEL Label of the H.L. B coef. to use during phased

refinement in refmac. NO default.

--hlc=LABEL Label of the H.L. C coef. to use during phased

refinement in refmac. NO default.

--hld=LABEL Label of the H.L. D coef. to use during phased

refinement in refmac. NO default.

--phiref=LABEL Label of the phase to be used for phased refinement in

refmac. Also requires to set fomref. No default

(ignored if HL. are given).

--fomref=LABEL Label of the FOM going with phiref, mandatory for

phiref to be used. No default.

--R-free=LABEL Label of the R-free set marker. NO default.

--refmac-B-sharpening=B-DECREASE

This set the sharpening of Refmac, so it 'artificialy'

decrease the B-factor of the dataset by setted amount.

--NCS-cross-completion

If present, Crude NCS Cross-Completion will be

attempted.

--New-chain-tracing If present, chain tracing will use hmain/pept,

otherwise cubes/pept_hmain.

--perform_extension If present, Extension_app will be used durring main

chain building.

--keep-log=EXENAME:EXENAME...

The executable for which the log file(s) should be

kept. Choose from list : (BLAST, GetPDB, Phaser,

Phaser2PDB, DataFile2PDB, DummyAll, MTZMaker, MTZ2PDB,

PDBStart, Refmac, ARP, HmainPept, CubesPepthmain,

Snow, SnowLongLoop, NCSCrudeGen). Default is NONE.

--keep-input=EXENAME:EXENAME...

The executable for which the input file(s) should be

kept. Default is NONE.

--keep-output=EXENAME:EXENAME...

The executable for which the output file(s) should be

kept. Default is NONE.

--max-build-cycles=NB-CYCLES-MAX

The number of building cycle after which we should

stop (whatever the completness).

--target-completness=PERCENT-COMPLETE

At which level of completness you want to finish by

hand (in percent).

--save-completness=PERCENT-COMPLETE

At which level of completness you want to save the

model (in percent).

--snow-docking=SCHEME-NAME

Which algorithm to use for sequence docking (one of

TopologyVector, RotamerDensity,

TopologyVectorThenRotamerDensityDocker).

--snow-scoring-scheme=SCHEME-NAME

Which topology vector scoring scheme should be used in

snow (one of EmpiricalFormula, FrequencyTable,

BayesLikelyhood).

--snow-force-use-sequence-prior

If present, forces SNOW to use frequence of AA in the

sequence as a prior-probability (you should AVOID it).

--build-loop=SCHEME-NAME

Which kind of loop to build after sequence docking

(Short, Long, Both, No). Default to 'Both'

--debug-decisions If present, more logging will be output to help

understanding/debugging the decisions.